RetrogeneDB ID: retro_dnov_469

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5105:235592..236247(-)
• Located in intron of: ENSDNOG00000012230

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSDNOG00000012921
• Aliases: None
• Description: ribosomal protein L10a [Source:HGNC Symbol;Acc:10299]

Sequence

>retro_dnov_469
AGCACCATGAGAAGCAAAGTGTGTTGCGACACCCTCTACCAGACAGTGTGGGAAGTCCTGCACAGGAATCAGCACAAGCG
CCAGAAGTTTTTGGAAACCACAGAGCTGCAGATCAGCTTCAAGAACCATGACCCTCAGAAGAACAAATGTTTCTTGGGCA
CCATCAGGCTCCAGTCTACTTAACCACCCAAAGTTCTCTGTGTGTGTCCCAGGAGACCAGCAGCACTGCAATGAAGCCAA
GGCAGTGGAGATGCCCCATACAGACATCAAAGCTCTAAAGAAACTCAACAAGAATAAAAAGCTGGTGAAAACTAGCAAGG
AAGTATGATGCCTTTTTTGGCCTGAGTCCCTGATTAAGTAGATTCCACGAATCCTTGGCCCAGGGCTGAATAAGCCTGGC
AAGTTTCCTTCTCTGCTGACCCACAATGAGAACATGGTGGTCAAAATTGATGAAGTGAAGTACACAGTCGAGTTCCAGAT
GAAGAAGTGGCTGTGTCTAGCTGCGGTGGTTGGCCATGTGACGATGACAGATGATGAGCTATGTACAACATCCACCTGGC
TGTCAACTTCCTGGTGTCACTGCTCAAGAAGAATTAGGAGAAATATCCGAGCTTTATACATCAACAACACCATGGACAAA
CCCCAGCACCTGTAC

Alignment

ORF - retro_dnov_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ATMSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKST-PRPKFSVCV
          .TM.SKV..DTLY..V.EVLH.NQ.KR.KFLET.ELQIS.KN.DPQK.K.F.GT.RL.ST...PKFSVCV
Retrocopy STMRSKVCCDTLYQTVWEVLHRNQHKRQKFLETTELQISFKNHDPQKNKCFLGTIRLQST>NHPKFSVCV

Parental  LGDQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSL
          .GDQQHC.EAKAV..PH.DI.ALKKLNKNKKLVK...K........ESLIK.IPRILGPGLNK.GKFPSL
Retrocopy PGDQQHCNEAKAVEMPHTDIKALKKLNKNKKLVK-TSKEV*CLFWPESLIK*IPRILGPGLNKPGKFPSL

Parental  LTHNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDEL-VYNIHLAVNFLVSLLKKN-WQNVRALY
          LTHNENMV.K.DEVK.T..FQMKK.LCLA..VGHV.MTDDEL..YNIHLAVNFLVSLLKKN...N.RALY
Retrocopy LTHNENMVVKIDEVKYTVEFQMKKWLCLAAVVGHVTMTDDEL<MYNIHLAVNFLVSLLKKN>RRNIRALY

Parental  IKSTMGKPQRLY
          I..TM.KPQ.LY
Retrocopy INNTMDKPQHLY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	0.00 RPM	508.34 RPM
SRP012922_cerebellum	0.00 RPM	227.65 RPM
SRP012922_heart	0.00 RPM	248.97 RPM
SRP012922_kidney	0.00 RPM	758.14 RPM
SRP012922_liver	0.00 RPM	261.47 RPM
SRP012922_lung	0.00 RPM	582.03 RPM
SRP012922_quadricep_muscle	0.00 RPM	318.65 RPM
SRP012922_spleen	0.00 RPM	713.32 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_469 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019494	4 retrocopies	retro_btau_138, retro_btau_1501, retro_btau_1634, retro_btau_87,
Dasypus novemcinctus	ENSDNOG00000012921	3 retrocopies	retro_dnov_157, retro_dnov_1917, retro_dnov_469 ,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Mus musculus	ENSMUSG00000037805	8 retrocopies	retro_mmus_1110, retro_mmus_1304, retro_mmus_1422, retro_mmus_149, retro_mmus_1737, retro_mmus_2038, retro_mmus_2652, retro_mmus_452,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Sus scrofa	ENSSSCG00000001543	7 retrocopies	retro_sscr_1169, retro_sscr_1174, retro_sscr_120, retro_sscr_246, retro_sscr_379, retro_sscr_461, retro_sscr_465,